Software for the integration of multiomics experiments in Bioconductor.
AffiliationGraduate School of Public Health & Health Policy, City University of New York, New York, New York
MetadataShow full item record
AbstractMultiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets. Cancer Res; 77(21); e39-42. ©2017 AACR.
CitationSoftware for the integration of multiomics experiments in Bioconductor. 2017, 77 (21):e39-e42 Cancer Res.
- The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.
- Authors: González-Beltrán A, Neumann S, Maguire E, Sansone SA, Rocca-Serra P
- Issue date: 2014
- The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.
- Authors: Lau JW, Lehnert E, Sethi A, Malhotra R, Kaushik G, Onder Z, Groves-Kirkby N, Mihajlovic A, DiGiovanna J, Srdic M, Bajcic D, Radenkovic J, Mladenovic V, Krstanovic D, Arsenijevic V, Klisic D, Mitrovic M, Bogicevic I, Kural D, Davis-Dusenbery B, Seven Bridges CGC Team.
- Issue date: 2017 Nov 1
- Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences.
- Authors: Hon J, Martínek T, Rajdl K, Lexa M
- Issue date: 2013 Aug 1
- The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research.
- Authors: Reynolds SM, Miller M, Lee P, Leinonen K, Paquette SM, Rodebaugh Z, Hahn A, Gibbs DL, Slagel J, Longabaugh WJ, Dhankani V, Reyes M, Pihl T, Backus M, Bookman M, Deflaux N, Bingham J, Pot D, Shmulevich I
- Issue date: 2017 Nov 1
- ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
- Authors: Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R
- Issue date: 2009 Oct 1